AimsThe aim was to investigate the intestinal community of Enterococcus faecalis from healthy confined non-industrialized chicken. Methods and ResultsA total of 206 E. faecalis isolates were collected from cloacal swabs. The prevalence of E. faecalis from two confined flocks was 83 and 96%, while only 44 and 13% in two fancy breeder flocks. A total of 204 isolates were characterized by pulsed-field-gel-electrophoresis (PFGE) where 40 strains were selected for multi-locus sequence typing (MLST). In all, 19 PFGE patterns and 14 STs were obtained. Four STs were identified in each of the two confined flocks, with one shared ST, while seven STs were identified in the two fancy breeder flocks. Only six of the identified STs had previously been registered in chicken. ConclusionThe majority of clonal lineages of E. faecalis associated with chicken reared in confinement and under backyard conditions were unrelated. Significance and Impact of the StudyThis study has provided new information on opportunistic E. faecalis in confined non-industrial chicken. Knowledge of population diversity and prevalence compared to conventional production is important to accesses, if certain clonal lineages are more likely to be associated with other intestinal E. faecalis lineages in chicken, and it is an important tool for gaining control of clones involved in disease and antibiotic resistance.